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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2024 Feb 20;80(Pt 3):325–329. doi: 10.1107/S2056989024001658

Crystal structure and Hirshfeld surface analysis of 4-oxo-3-phenyl-2-sulfanyl­idene-5-(thio­phen-2-yl)-3,4,7,8,9,10-hexa­hydro-2H-pyrido[1,6-a:2,3-d′]di­pyrimidine-6-carbo­nitrile

Farid N Naghiyev a, Victor N Khrustalev b,c, Mehmet Akkurt d,*, Huseyn M Mamedov e, Ajaya Bhattarai f,*, Ali N Khalilov g,a, İbrahim G Mamedov a
Editor: B Therrienh
PMCID: PMC10915664  PMID: 38456056

In the title compound, mol­ecular pairs are linked by N—H⋯N hydrogen bonds along the c-axis direction and C—H⋯S and C—H⋯O hydrogen bonds along the b-axis direction, with Inline graphic (12) and Inline graphic (16) motifs, respectively, thus forming layers parallel to the (10 Inline graphic ) plane. In addition, C=S⋯π and C≡N⋯π inter­actions between the layers ensure crystal cohesion.

Keywords: crystal structure, hydrogen bonds, heterocycle, Hirshfeld surface analysis

Abstract

In the title compound, C21H15N5OS2, mol­ecular pairs are linked by N—H⋯N hydrogen bonds along the c-axis direction and C—H⋯S and C—H⋯O hydrogen bonds along the b-axis direction, with R 2 2(12) and R 2 2(16) motifs, respectively, thus forming layers parallel to the (10 Inline graphic ) plane. In addition, C=S⋯π and C≡N⋯π inter­actions between the layers ensure crystal cohesion. The Hirshfeld surface analysis indicates that the major contributions to the crystal packing are H⋯H (43.0%), C⋯H/H⋯C (16.9%), N⋯H/H⋯N (11.3%) and S⋯H/H⋯S (10.9%) inter­actions.

1. Chemical context

Heterocyclic systems are an important group of organic compounds. Synthetic chemistry has grown abundantly over the past few decades and recently developed heterocyclic systems have found diverse research and commercial applications, especially in the pharmaceutical and chemical industries (Maharramov et al., 2021 ▸, 2022 ▸; Erenler et al., 2022 ▸; Akkurt et al., 2023 ▸). These compounds have also found wide implementations in diverse fields of chemical science, including in coordination chemistry (Gurbanov et al., 2021 ▸; Mahmoudi et al., 2021 ▸), medicinal chemistry (Dönmez & Türkyılmaz, 2022 ▸; Askerova, 2022 ▸) and materials science (Velásquez et al., 2019 ▸; Afkhami et al., 2019 ▸). Pyridodi­pyrimidines are a specific group of heterocyclic systems that contain a fused tricyclic system with four or five nitro­gen atoms in their structure. These compounds are analogues of tetra- or penta-aza-anthracene or phenanthrene and usually exist in either a linear or an angular form. This moiety is present in drugs, and in recent years it has been studied in the development of new active compounds, as evidenced by numerous publications (Yousif et al., 2021 ▸; Sobhi & Faisal, 2023 ▸). Derivatives comprising the pyridodi­pyrimidine skeleton show diverse biological activities, such as anti­tumour activity, inhibiting di­hydro­folate reductases or tyrosine kinases, anti-inflammatory activity, anti­hypertensive activity, anti­bacterial activity, anti­convulsant activity, calcium channel antagonist activity, etc. Historical and modern synthetic approaches for the preparation of these systems have been reviewed recently (Atalay et al., 2022 ▸; Hammouda et al., 2023 ▸). Thus, in the framework of our studies in heterocyclic chemistry (Naghiyev et al., 2020 ▸, 2021 ▸, 2022 ▸; Khalilov et al., 2022 ▸), we report the synthesis and characterization of the title compound, 4-oxo-3-phenyl-2-sulfanyl­idene-5-(thio­phen-2-yl)-3,4,7,8,9,10-hexa­hydro-2H-pyrido[1,6-a:2,3-d′]di­pyrimidine-6-carbo­nitrile. 1.

2. Structural commentary

The thio­phene ring (S2/C17–C20; Fig. 1 ▸) in the title compound is disordered over two sites in a 0.787 (3):0.213 (3) ratio by an approximate rotation of 180° about the C5—C17 bond. The phenyl ring (C11-C16) is also disordered over two positions with the same ratio. In the 1,3-diazinane ring (N7/N11/C6A/C8–C10), the middle carbon atom (C9) is similarly disordered. The ten-membered 2,3,4,8-tetra­hydro­pyrido[2,3-d]pyrimidine ring system (N1/N3/N11/C1A/C2/C4/C4A/C5/C6/C6A) has a nearly planar conformation (r.m.s. deviation = 0.1183 Å). The dihedral angles between the major and minor components of the disordered phenyl (C11–C16 and C11/C12–C16A) and thio­phene (S2/C17–C20 and S2A/C17/C18A–C20A) rings are 20.3 (9) and 6.7 (7)°, respectively, and these disordered components make dihedral angles of 71.9 (3), 88.0 (4)° and 64.0 (2), 70.6 (4)°, respectively, with the ten-membered ring system. The geometric parameters are normal and comparable to those of related compounds described in the Database survey section.

Figure 1.

Figure 1

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The mol­ecular structure, showing the atom labelling and displacement ellipsoids drawn at the 30% probability level. Only the major component of the disorder is shown.

3. Supra­molecular features and Hirshfeld surface analysis

In the crystal, mol­ecular pairs are linked by N—H⋯N hydrogen bonds along the c-axis direction and C—H⋯S and C—H⋯O hydrogen bonds along the b-axis direction, with Inline graphic (12) and Inline graphic (16) motifs, respectively (Bernstein et al., 1995 ▸; Table 1 ▸; Fig. 2 ▸). They form layers parallel to the (10 Inline graphic ) plane. Crystal cohesion between the layers is ensured by C=S⋯π and C≡N⋯π inter­actions [(C2)S1⋯Cg6a = 3.4304 (9) Å, C2(S1)⋯Cg6a = 3.643 (2) Å, C2=S1⋯Cg6a = 83.57 (8)°; (C21)N21⋯Cg5b = 3.330 (4) Å, C21(N21)⋯Cg5b = 3.613 (4) Å, C21≡N21⋯Cg5b = 94.91 (15)°; symmetry codes: (a) −1 + x, y, z; (b) 2 − x, 1 − y, 2 − z; Cg5 and Cg6 are the centroids of the N7/N11/C6A/C8/C9A/C10 and N11/C1A/C4A/C5/C6/C6A rings] (Table 1 ▸; Fig. 3 ▸).

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N7—H7⋯N21i 0.89 (2) 2.14 (2) 2.976 (3) 157 (2)
C9—H9B⋯O1ii 0.99 2.34 3.197 (3) 144
C16—H16⋯S2A iii 0.95 2.73 3.58 (2) 149
C19—H19⋯S1iv 0.95 2.76 3.652 (5) 156
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Symmetry codes: (i) Inline graphic ; (ii) Inline graphic ; (iii) Inline graphic ; (iv) Inline graphic .

Figure 2.

Figure 2

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View of the N—H⋯N, C—H⋯O and C—H⋯S hydrogen bonds down the a-axis. Only the major component of the disorder and the H atoms involved are shown.

Figure 3.

Figure 3

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View of the π–π and C—N⋯π and C—S⋯π inter­actions down the b-axis. Only the major component of the disorder is shown. All H atoms are omitted for clarity.

Two-dimensional fingerprint plots and Hirshfeld surfaces were produced using Crystal Explorer 17.5 (Spackman et al., 2021 ▸) to qu­antify the inter­molecular inter­actions. The d norm surfaces are mapped over a fixed colour scale from −0.4663 (red) to +1.2045 (blue) a.u. Red spots on the surface corres­pond to N—H⋯N, C—H⋯O and C—H⋯S inter­actions (Tables 1 ▸ and 2 ▸; Fig. 4 ▸ a,b). The most significant inter­atomic contact is H⋯H, because it contributes the most to the crystal packing (43.0%, Fig. 5 ▸ b). Other significant contributions are from C⋯H/H⋯C (16.9%, Fig. 5 ▸ c), N⋯H/H⋯N (11.3%, Fig. 5 ▸ d) and S⋯H/H⋯S (10.9%, Fig. 5 ▸ e) inter­actions. The following inter­actions have minor contributions: O⋯H/H⋯O (7.2%), C⋯C (3.4%), N⋯C/C⋯N (3.1%), S⋯C/C⋯S (2.0%), N⋯N (1.3%) and S⋯N/N⋯S (0.8%).

Table 2. Summary of short inter­atomic contacts (Å).

Atoms belonging to the minor disorder components are indicated by an asterisk (*).

*H16A⋯O1 2.34 −1 + x, y, z
*H9B⋯O1 2.34 Inline graphic  − x, Inline graphic  + y, Inline graphic  − z
*H9C⋯*H15 1.87 Inline graphic  − x, Inline graphic  + y, Inline graphic  − z
*H13⋯S1 2.93 −x, 1 − y, 1 − z
*H18A⋯*H8D 1.87 2 − x, 1 − y, 2 − z
H7⋯N21 2.14 3 − x, 1 − y, 2 − z
*H13A⋯*H20 2.26 − Inline graphic  + x, Inline graphic  − y, − Inline graphic  + z
*H20A⋯*H14 2.58 Inline graphic  + x, Inline graphic  − y, Inline graphic  + z
*H13A⋯*H12 2.46 1 − x, 1 − y, 1 − z
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Figure 4.

Figure 4

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(a) Front and (b) back sides of the three-dimensional Hirshfeld surface of the compound mapped over d norm.

Figure 5.

Figure 5

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The two-dimensional fingerprint plots of the title compound, showing (a) all inter­actions, and delineated into (b) H⋯H, (c) C⋯H/H⋯C, (d) N⋯H/H⋯N and (e) S⋯H/H⋯S inter­actions. [d e and d i represent the distances from a point on the Hirshfeld surface to the nearest atoms outside (external) and inside (inter­nal) the surface, respectively].

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.43, last update November 2022; Groom et al., 2016 ▸) for the central ten-membered ring 2,3,4,8-tetra­hydro­pyrido[2,3-d]pyrimidine yielded four hits, viz. 11-(amino­methyl­idene)-8,9,10,11-tetra­hydro­pyrido[2′,3′:4,5]pyrimido[1,2-a]aze­pin-5(7H)-one (CSD refcode HECLUZ; Khodjaniyazov et al., 2017 ▸), 7-amino-1,3-dimethyl-5-(4-nitro­phen­yl)-2,4-dioxo-1,2,3,4-tetra­hydro­pyrido(2,3-d)pyrimidine-6-carbo­nitrile (NIFBUA; Zhou et al., 2007 ▸), 3-(4-fluoro­phen­yl)-1,5,7-tri­methyl-1,2,3,4-tetra­hydro­pyrido(2,3-d)pyrimidine-2,4-dione (Patel et al., 2007 ▸) and 2-(4-chloro-3-methyl­phen­oxy)-3-(4-chloro­phen­yl)-5-methyl-8,9,10,11-tetra­hydro-1-benzothieno(2′,3′:2,3)pyrido(4,5-d)pyrimidin-4(3H)-one di­chloro­methane solvate (JAYKOK; Liu et al., 2005 ▸). In HECLUZ, hydrogen bonds with a 16-membered ring and three chain motifs are generated by N—H⋯N and N—H⋯O contacts. The amino group is located close to the nitro­gen atoms N1 and N8 of an inversion-related mol­ecule, forming hydrogen bonds with Inline graphic (4) and Inline graphic (12) graph-set motifs. This amino group also forms a hydrogen bond with the C=O oxygen atom of a mol­ecule translated along the a-axis direction, which links the mol­ecules into Inline graphic (16) rings. Hydrogen-bonded chains are formed along [100] by alternating Inline graphic (12) and Inline graphic (16) rings. These chains are stabilized by inter­molecular π–π stacking inter­actions between the pyridine and pyrimidine rings [centroid–centroid distance = 3.669 (2) Å; symmetry operation 1 − x, 1 − y, 1 − z]. In NIFBUA, mol­ecules are linked by N—H⋯O, C—H⋯O and C—H⋯N hydrogen bonds, forming a three-dimensional network. In HIFREU, a diverse set of weak inter­molecular C—H⋯π, π–π and C—H⋯O inter­actions link the mol­ecules into sheets. The C—H⋯O inter­actions generate centrosymmetric rings with an Inline graphic (14) graph-set motif and chains with a C(8) motif. In JAYKOK, the mol­ecules are connected in the form of zigzag ribbons along the b-axis direction by C—H⋯π and C—Cl⋯π inter­actions. van der Waals inter­actions between the ribbons ensure the cohesion of the crystal structure.

5. Synthesis and crystallization

A solution of 6-amino-9-iso­cyano-8-(thio­phen-2-yl)-3,4-di­hydro-2H-pyrido[1,2-a]pyrimidine-7-carbo­nitrile (3.5 mmol) and potassium hydroxide (3.5 mmol) was stirred in DMF (25 mL) for 2 h at room temperature. Phenyl iso­thio­cyanate (3.5 mmol) was added dropwise to the reaction mixture and it was stirred for 2 h. The reaction mixture was kept for 48 h at room temperature and acidified with 5 mL (37% HCl) solution. The precipitate was filtered and recrystallized from an ethanol water (3:1 ratio) solution. The title compound was obtained in 77% yield, m.p. 469–470 K.

1H NMR (300 MHz, DMSO-d 6, ppm.): 1.95 (m, 2H, CH2); 3.59 (t, 2H, CH2); 4.06 (t, 2H, CH2); 7.31–7.51 (m, 6H, 5CHarom. + 1H, thioph.); 7.54 (d, 1H, thioph.); 7.89 (d, 1H, thioph.); 8.40 (s, 1H, NH). 13C NMR (75 MHz, DMSO-d 6, ppm): 19.84 (CH2), 41.22 (CH2), 43.68 (CH2), 53.58 (=Ctert.), 98.75 (=Ctert.), 119.67 (CN), 122.94 (2CHarom.), 126.28 (CHarom.), 126.91 (Cthioph.), 128.43 (CHthioph.), 129.29 (CHthioph.), 131.64 (CHthioph.), 132.72 (2CHarom.), 135.97 (Carom.), 147.11 (=Ctert.), 149.45 (=Ctert.), 152.32 (N—C=O), 161.60 (=Ctert.), 179.85 (N—C=S).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3 ▸. The thio­phene ring (S2/C17–C20) is disordered over two sites related by an approximate rotation of 180° about the C5—C17 bond in a 0.787 (3):0.213 (3) ratio. The phenyl ring (C11–C16) is also disordered over two sites in a 0.787 (3):0.213 (3) ratio. The minor occupancy component of the phenyl ring was restrained to be planar, using FLAT commands. The middle carbon atom (C9) in the 1,3-diazinane ring (N7/N11/C6A/C8–C10) is similarly disordered. EADP in SHELXL was used for the U ij values of equivalent atom pairs (e.g., S2 and S2A ) and SADI was employed for the disordered components to restrain the bond lengths and angles of the major and minor components to be the same within an e.s.d. of 0.02 Å, to ensure chemically reasonable bond length and angle values. The C-bound H atoms were placed in calculated positions (0.95–0.99 Å) and refined as riding atoms with U iso(H) = 1.2U eq(C). The N-bound H atoms were located in a difference map and freely refined.

Table 3. Experimental details.

Crystal data
Chemical formula C21H15N5OS2
M r 417.50
Crystal system, space group Monoclinic, P21/n
Temperature (K) 100
a, b, c (Å) 5.63465 (3), 18.02763 (13), 18.40115 (12)
β (°) 97.1649 (6)
V (Å3) 1854.58 (2)
Z 4
Radiation type Cu Kα
μ (mm−1) 2.81
Crystal size (mm) 0.31 × 0.05 × 0.05
 
Data collection
Diffractometer XtaLAB Synergy, Dualflex, HyPix
Absorption correction Gaussian (CrysAlis PRO; Rigaku OD, 2022 ▸)
T min, T max 0.495, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 39427, 3946, 3842
R int 0.032
(sin θ/λ)max (Å−1) 0.634
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.047, 0.130, 1.09
No. of reflections 3946
No. of parameters 299
No. of restraints 16
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.46, −0.35
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Computer programs: CrysAlis PRO (Rigaku OD, 2022 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL (Sheldrick, 2015b ▸), ORTEP-3 for Windows (Farrugia, 2012 ▸) and PLATON (Spek, 2020 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989024001658/tx2082sup1.cif

e-80-00325-sup1.cif (1.2MB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989024001658/tx2082Isup2.hkl

e-80-00325-Isup2.hkl (314.7KB, hkl)
e-80-00325-Isup3.cml (7.2KB, cml)

Supporting information file. DOI: 10.1107/S2056989024001658/tx2082Isup3.cml

CCDC reference: 2333770

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

Authors contributions are as follows. Conceptualization, IGM, ANK and AMM; methodology, IB and MA; investigation, VNK and FNN; writing (original draft), MA, AB and ANK,; writing (review and editing of the manuscript), MA and ANK; visualization, MA, IGM and FNN; funding acquisition, HMM, AB and FNN; resources, AB, VNK and MA; supervision, MA and ANK.

supplementary crystallographic information

Crystal data

C21H15N5OS2 F(000) = 864
Mr = 417.50 Dx = 1.495 Mg m−3
Monoclinic, P21/n Cu Kα radiation, λ = 1.54184 Å
a = 5.63465 (3) Å Cell parameters from 25424 reflections
b = 18.02763 (13) Å θ = 2.4–77.5°
c = 18.40115 (12) Å µ = 2.81 mm−1
β = 97.1649 (6)° T = 100 K
V = 1854.58 (2) Å3 Needle, orange
Z = 4 0.31 × 0.05 × 0.05 mm
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Data collection

XtaLAB Synergy, Dualflex, HyPix diffractometer 3842 reflections with I > 2σ(I)
Radiation source: micro-focus sealed X-ray tube Rint = 0.032
φ and ω scans θmax = 77.8°, θmin = 3.5°
Absorption correction: gaussian (CrysAlisPro; Rigaku OD, 2022) h = −7→6
Tmin = 0.495, Tmax = 1.000 k = −22→22
39427 measured reflections l = −23→23
3946 independent reflections
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Refinement

Refinement on F2 Primary atom site location: difference Fourier map
Least-squares matrix: full Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047 Hydrogen site location: mixed
wR(F2) = 0.130 H atoms treated by a mixture of independent and constrained refinement
S = 1.09 w = 1/[σ2(Fo2) + (0.0624P)2 + 1.7979P] where P = (Fo2 + 2Fc2)/3
3946 reflections (Δ/σ)max = 0.003
299 parameters Δρmax = 0.46 e Å−3
16 restraints Δρmin = −0.34 e Å−3
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Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
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Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq Occ. (<1)
S1 0.02652 (9) 0.56892 (3) 0.69073 (3) 0.03115 (15)
S2 0.72669 (14) 0.28256 (5) 0.87597 (5) 0.0385 (3) 0.787 (3)
S2A 1.1539 (16) 0.3143 (6) 0.8247 (7) 0.0342 (13) 0.213 (3)
O1 0.5802 (3) 0.35719 (8) 0.72211 (8) 0.0330 (3)
N1 0.4413 (3) 0.57036 (9) 0.77539 (9) 0.0271 (4)
C1A 0.6322 (3) 0.53620 (11) 0.80803 (10) 0.0254 (4)
C2 0.2865 (4) 0.53163 (11) 0.72644 (11) 0.0270 (4)
N3 0.3507 (3) 0.46068 (10) 0.70538 (9) 0.0281 (4)
C4 0.5389 (4) 0.41982 (11) 0.74252 (11) 0.0262 (4)
C4A 0.6778 (3) 0.45923 (11) 0.80310 (10) 0.0251 (4)
C5 0.8706 (3) 0.42724 (11) 0.84720 (11) 0.0255 (4)
C6 1.0250 (3) 0.47366 (11) 0.89208 (11) 0.0266 (4)
C6A 0.9921 (4) 0.55219 (11) 0.89144 (10) 0.0263 (4)
N7 1.1448 (3) 0.59618 (10) 0.93177 (10) 0.0320 (4)
H7 1.278 (3) 0.5768 (15) 0.9549 (15) 0.048 (8)*
C8 1.1322 (4) 0.67714 (12) 0.93061 (14) 0.0378 (5)
H8A 1.2951 0.6985 0.9390 0.045* 0.915 (5)
H8B 1.0405 0.6951 0.9697 0.045* 0.915 (5)
H8C 1.2530 0.6960 0.9005 0.045* 0.085 (5)
H8D 1.1768 0.6956 0.9812 0.045* 0.085 (5)
C9 1.0108 (5) 0.70013 (13) 0.85711 (13) 0.0335 (6) 0.915 (5)
H9A 1.1097 0.6855 0.8186 0.040* 0.915 (5)
H9B 0.9914 0.7547 0.8555 0.040* 0.915 (5)
C9A 0.899 (3) 0.7088 (11) 0.9022 (12) 0.0335 (6) 0.085 (5)
H9C 0.9231 0.7592 0.8831 0.040* 0.085 (5)
H9D 0.8002 0.7134 0.9429 0.040* 0.085 (5)
C10 0.7676 (4) 0.66313 (11) 0.84300 (12) 0.0326 (5)
H10A 0.6634 0.6814 0.8786 0.039* 0.915 (5)
H10B 0.6911 0.6756 0.7931 0.039* 0.915 (5)
H10C 0.8202 0.6784 0.7959 0.039* 0.085 (5)
H10D 0.5951 0.6749 0.8404 0.039* 0.085 (5)
N11 0.7967 (3) 0.58104 (9) 0.85025 (9) 0.0263 (4)
C11 0.2322 (4) 0.42875 (12) 0.63790 (12) 0.0327 (5)
C12 0.2858 (14) 0.4548 (5) 0.5706 (3) 0.0463 (17) 0.596 (9)
H12 0.4075 0.4911 0.5692 0.056* 0.596 (9)
C13 0.1650 (13) 0.4288 (4) 0.5059 (3) 0.0523 (15) 0.596 (9)
H13 0.2012 0.4474 0.4603 0.063* 0.596 (9)
C14 −0.0112 (19) 0.3748 (6) 0.5082 (14) 0.0496 (16) 0.596 (9)
H14 −0.0937 0.3561 0.4638 0.060* 0.596 (9)
C15 −0.067 (4) 0.3481 (8) 0.5740 (11) 0.0416 (17) 0.596 (9)
H15 −0.1855 0.3109 0.5753 0.050* 0.596 (9)
C16 0.0531 (17) 0.3765 (6) 0.6387 (12) 0.0348 (18) 0.596 (9)
H16 0.0109 0.3597 0.6843 0.042* 0.596 (9)
C12A 0.358 (2) 0.4353 (7) 0.5772 (6) 0.0463 (17) 0.404 (9)
H12A 0.5096 0.4589 0.5808 0.056* 0.404 (9)
C13A 0.253 (2) 0.4061 (6) 0.5123 (5) 0.0523 (15) 0.404 (9)
H13A 0.3295 0.4115 0.4695 0.063* 0.404 (9)
C14A 0.036 (3) 0.3687 (9) 0.508 (2) 0.0496 (16) 0.404 (9)
H14A −0.0360 0.3486 0.4627 0.060* 0.404 (9)
C15A −0.072 (6) 0.3615 (12) 0.5701 (17) 0.0416 (17) 0.404 (9)
H15A −0.2206 0.3359 0.5668 0.050* 0.404 (9)
C16A 0.023 (3) 0.3894 (10) 0.6378 (19) 0.0348 (18) 0.404 (9)
H16A −0.0513 0.3819 0.6808 0.042* 0.404 (9)
C17 0.9179 (4) 0.34677 (11) 0.84955 (11) 0.0281 (4)
C18 1.1076 (17) 0.3082 (6) 0.8292 (8) 0.0342 (13) 0.787 (3)
H18 1.2341 0.3338 0.8103 0.041* 0.787 (3)
C19 1.1145 (8) 0.2330 (3) 0.8361 (3) 0.0375 (9) 0.787 (3)
H19 1.2400 0.2018 0.8242 0.045* 0.787 (3)
C20 0.9166 (7) 0.21043 (19) 0.8622 (3) 0.0430 (9) 0.787 (3)
H20 0.8838 0.1600 0.8722 0.052* 0.787 (3)
C18A 0.781 (3) 0.2960 (8) 0.8922 (9) 0.0385 (3) 0.213 (3)
H18A 0.6662 0.3094 0.9235 0.046* 0.213 (3)
C19A 0.853 (3) 0.2263 (9) 0.8774 (11) 0.0430 (9) 0.213 (3)
H19A 0.7666 0.1827 0.8860 0.052* 0.213 (3)
C20A 1.060 (4) 0.2264 (10) 0.8495 (14) 0.0375 (9) 0.213 (3)
H20A 1.1489 0.1825 0.8436 0.045* 0.213 (3)
C21 1.2205 (4) 0.44413 (11) 0.94061 (11) 0.0286 (4)
N21 1.3785 (3) 0.42360 (10) 0.98069 (11) 0.0342 (4)
Open in a new tab

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
S1 0.0299 (3) 0.0326 (3) 0.0293 (3) 0.00388 (19) −0.00271 (19) 0.00214 (18)
S2 0.0288 (5) 0.0342 (5) 0.0513 (5) −0.0065 (3) −0.0005 (3) 0.0115 (3)
S2A 0.017 (3) 0.0302 (16) 0.0576 (16) −0.0004 (19) 0.015 (2) 0.0102 (12)
O1 0.0358 (8) 0.0268 (7) 0.0350 (8) 0.0007 (6) −0.0007 (6) −0.0018 (6)
N1 0.0289 (8) 0.0287 (8) 0.0225 (8) 0.0041 (6) −0.0015 (6) 0.0002 (6)
C1A 0.0269 (9) 0.0275 (10) 0.0214 (8) 0.0021 (7) 0.0015 (7) 0.0025 (7)
C2 0.0296 (9) 0.0283 (10) 0.0228 (9) 0.0001 (8) 0.0025 (7) 0.0028 (7)
N3 0.0302 (8) 0.0286 (8) 0.0243 (8) 0.0005 (7) −0.0007 (6) −0.0004 (6)
C4 0.0265 (9) 0.0262 (9) 0.0258 (9) −0.0008 (7) 0.0022 (7) 0.0031 (7)
C4A 0.0251 (9) 0.0260 (9) 0.0239 (9) −0.0007 (7) 0.0013 (7) 0.0038 (7)
C5 0.0243 (9) 0.0266 (9) 0.0255 (9) −0.0003 (7) 0.0024 (7) 0.0055 (7)
C6 0.0263 (9) 0.0263 (10) 0.0260 (9) 0.0016 (7) −0.0005 (7) 0.0043 (7)
C6A 0.0276 (9) 0.0280 (10) 0.0227 (9) 0.0024 (8) 0.0004 (7) 0.0015 (7)
N7 0.0318 (9) 0.0271 (9) 0.0341 (9) 0.0027 (7) −0.0078 (7) −0.0011 (7)
C8 0.0392 (12) 0.0266 (11) 0.0440 (12) 0.0024 (9) −0.0090 (10) −0.0045 (9)
C9 0.0430 (13) 0.0240 (11) 0.0316 (12) 0.0028 (9) −0.0031 (9) 0.0007 (9)
C9A 0.0430 (13) 0.0240 (11) 0.0316 (12) 0.0028 (9) −0.0031 (9) 0.0007 (9)
C10 0.0396 (11) 0.0239 (10) 0.0314 (10) 0.0067 (8) −0.0072 (8) −0.0012 (8)
N11 0.0300 (8) 0.0240 (8) 0.0233 (8) 0.0042 (6) −0.0024 (6) 0.0001 (6)
C11 0.0369 (11) 0.0320 (11) 0.0287 (10) −0.0004 (8) 0.0018 (9) −0.0019 (8)
C12 0.051 (4) 0.054 (4) 0.0352 (18) −0.016 (3) 0.008 (2) −0.004 (2)
C13 0.061 (4) 0.067 (4) 0.0287 (17) −0.010 (3) 0.003 (3) −0.001 (2)
C14 0.056 (4) 0.053 (2) 0.0363 (13) −0.010 (2) −0.005 (4) −0.007 (2)
C15 0.0428 (16) 0.034 (5) 0.045 (2) −0.007 (4) −0.0086 (15) 0.004 (3)
C16 0.031 (3) 0.037 (4) 0.0352 (13) 0.003 (3) −0.001 (3) 0.004 (4)
C12A 0.051 (4) 0.054 (4) 0.0352 (18) −0.016 (3) 0.008 (2) −0.004 (2)
C13A 0.061 (4) 0.067 (4) 0.0287 (17) −0.010 (3) 0.003 (3) −0.001 (2)
C14A 0.056 (4) 0.053 (2) 0.0363 (13) −0.010 (2) −0.005 (4) −0.007 (2)
C15A 0.0428 (16) 0.034 (5) 0.045 (2) −0.007 (4) −0.0086 (15) 0.004 (3)
C16A 0.031 (3) 0.037 (4) 0.0352 (13) 0.003 (3) −0.001 (3) 0.004 (4)
C17 0.0271 (9) 0.0238 (9) 0.0315 (10) −0.0025 (7) −0.0044 (8) 0.0056 (8)
C18 0.017 (3) 0.0302 (16) 0.0576 (16) −0.0004 (19) 0.015 (2) 0.0102 (12)
C19 0.042 (3) 0.0268 (14) 0.042 (3) 0.0073 (15) −0.0043 (15) −0.0022 (13)
C20 0.043 (3) 0.0223 (18) 0.059 (2) −0.0055 (14) −0.0132 (18) 0.0046 (15)
C18A 0.0288 (5) 0.0342 (5) 0.0513 (5) −0.0065 (3) −0.0005 (3) 0.0115 (3)
C19A 0.043 (3) 0.0223 (18) 0.059 (2) −0.0055 (14) −0.0132 (18) 0.0046 (15)
C20A 0.042 (3) 0.0268 (14) 0.042 (3) 0.0073 (15) −0.0043 (15) −0.0022 (13)
C21 0.0295 (10) 0.0248 (9) 0.0305 (10) −0.0006 (8) −0.0007 (8) 0.0024 (8)
N21 0.0330 (9) 0.0297 (9) 0.0369 (10) 0.0020 (7) −0.0076 (8) 0.0026 (7)
Open in a new tab

Geometric parameters (Å, º)

S1—C2 1.670 (2) C10—H10C 0.9900
S2—C17 1.693 (2) C10—H10D 0.9900
S2—C20 1.723 (4) C11—C16A 1.377 (13)
S2A—C17 1.572 (9) C11—C16 1.382 (9)
S2A—C20A 1.750 (17) C11—C12 1.393 (7)
O1—C4 1.221 (2) C11—C12A 1.400 (10)
N1—C1A 1.318 (3) C12—C13 1.377 (7)
N1—C2 1.365 (3) C12—H12 0.9500
C1A—N11 1.392 (3) C13—C14 1.395 (9)
C1A—C4A 1.416 (3) C13—H13 0.9500
C2—N3 1.397 (3) C14—C15 1.374 (9)
N3—C4 1.398 (3) C14—H14 0.9500
N3—C11 1.453 (3) C15—C16 1.391 (9)
C4—C4A 1.464 (3) C15—H15 0.9500
C4A—C5 1.397 (3) C16—H16 0.9500
C5—C6 1.400 (3) C12A—C13A 1.370 (11)
C5—C17 1.475 (3) C12A—H12A 0.9500
C6—C6A 1.428 (3) C13A—C14A 1.389 (13)
C6—C21 1.431 (3) C13A—H13A 0.9500
C6A—N7 1.327 (3) C14A—C15A 1.369 (14)
C6A—N11 1.360 (2) C14A—H14A 0.9500
N7—C8 1.461 (3) C15A—C16A 1.386 (13)
N7—H7 0.888 (9) C15A—H15A 0.9500
C8—C9A 1.468 (16) C16A—H16A 0.9500
C8—C9 1.496 (3) C17—C18 1.366 (10)
C8—H8A 0.9900 C17—C18A 1.483 (14)
C8—H8B 0.9900 C18—C19 1.361 (11)
C8—H8C 0.9900 C18—H18 0.9500
C8—H8D 0.9900 C19—C20 1.332 (5)
C9—C10 1.517 (3) C19—H19 0.9500
C9—H9A 0.9900 C20—H20 0.9500
C9—H9B 0.9900 C18A—C19A 1.359 (17)
C9A—C10 1.487 (16) C18A—H18A 0.9500
C9A—H9C 0.9900 C19A—C20A 1.329 (16)
C9A—H9D 0.9900 C19A—H19A 0.9500
C10—N11 1.493 (3) C20A—H20A 0.9500
C10—H10A 0.9900 C21—N21 1.145 (3)
C10—H10B 0.9900
C17—S2—C20 92.57 (16) H10C—C10—H10D 107.3
C17—S2A—C20A 88.1 (8) C6A—N11—C1A 121.72 (17)
C1A—N1—C2 118.67 (17) C6A—N11—C10 120.07 (17)
N1—C1A—N11 115.60 (17) C1A—N11—C10 117.89 (16)
N1—C1A—C4A 124.97 (18) C16—C11—C12 118.6 (10)
N11—C1A—C4A 119.43 (17) C16A—C11—C12A 124.1 (15)
N1—C2—N3 119.04 (17) C16A—C11—N3 120.5 (14)
N1—C2—S1 120.70 (15) C16—C11—N3 121.3 (9)
N3—C2—S1 120.25 (15) C12—C11—N3 119.9 (4)
C2—N3—C4 123.61 (17) C12A—C11—N3 115.1 (5)
C2—N3—C11 119.51 (17) C13—C12—C11 121.0 (6)
C4—N3—C11 116.66 (17) C13—C12—H12 119.5
O1—C4—N3 119.91 (18) C11—C12—H12 119.5
O1—C4—C4A 125.36 (18) C12—C13—C14 119.2 (12)
N3—C4—C4A 114.69 (17) C12—C13—H13 120.4
C5—C4A—C1A 120.10 (18) C14—C13—H13 120.4
C5—C4A—C4 123.05 (18) C15—C14—C13 121 (2)
C1A—C4A—C4 116.12 (17) C15—C14—H14 119.6
C4A—C5—C6 118.50 (18) C13—C14—H14 119.6
C4A—C5—C17 123.21 (18) C14—C15—C16 119 (2)
C6—C5—C17 118.29 (17) C14—C15—H15 120.5
C5—C6—C6A 121.15 (18) C16—C15—H15 120.5
C5—C6—C21 121.27 (18) C11—C16—C15 121.3 (17)
C6A—C6—C21 117.58 (18) C11—C16—H16 119.3
N7—C6A—N11 120.44 (18) C15—C16—H16 119.3
N7—C6A—C6 120.91 (18) C13A—C12A—C11 117.1 (10)
N11—C6A—C6 118.63 (18) C13A—C12A—H12A 121.4
C6A—N7—C8 124.19 (18) C11—C12A—H12A 121.4
C6A—N7—H7 119 (2) C12A—C13A—C14A 121.3 (19)
C8—N7—H7 116 (2) C12A—C13A—H13A 119.3
N7—C8—C9A 115.6 (8) C14A—C13A—H13A 119.3
N7—C8—C9 107.80 (18) C15A—C14A—C13A 118 (3)
N7—C8—H8A 110.1 C15A—C14A—H14A 120.8
C9—C8—H8A 110.1 C13A—C14A—H14A 120.8
N7—C8—H8B 110.1 C14A—C15A—C16A 124 (3)
C9—C8—H8B 110.1 C14A—C15A—H15A 118.2
H8A—C8—H8B 108.5 C16A—C15A—H15A 118.2
N7—C8—H8C 108.4 C11—C16A—C15A 115 (3)
C9A—C8—H8C 108.4 C11—C16A—H16A 122.5
N7—C8—H8D 108.4 C15A—C16A—H16A 122.5
C9A—C8—H8D 108.4 C18—C17—C5 129.6 (5)
H8C—C8—H8D 107.4 C5—C17—C18A 121.3 (6)
C8—C9—C10 109.5 (2) C5—C17—S2A 120.9 (4)
C8—C9—H9A 109.8 C18A—C17—S2A 116.0 (7)
C10—C9—H9A 109.8 C18—C17—S2 106.2 (5)
C8—C9—H9B 109.8 C5—C17—S2 124.18 (16)
C10—C9—H9B 109.8 C19—C18—C17 119.7 (7)
H9A—C9—H9B 108.2 C19—C18—H18 120.2
C8—C9A—C10 112.8 (12) C17—C18—H18 120.2
C8—C9A—H9C 109.0 C20—C19—C18 108.8 (5)
C10—C9A—H9C 109.0 C20—C19—H19 125.6
C8—C9A—H9D 109.0 C18—C19—H19 125.6
C10—C9A—H9D 109.0 C19—C20—S2 112.7 (3)
H9C—C9A—H9D 107.8 C19—C20—H20 123.7
C9A—C10—N11 116.4 (8) S2—C20—H20 123.7
N11—C10—C9 109.50 (17) C19A—C18A—C17 106.0 (13)
N11—C10—H10A 109.8 C19A—C18A—H18A 127.0
C9—C10—H10A 109.8 C17—C18A—H18A 127.0
N11—C10—H10B 109.8 C20A—C19A—C18A 112.1 (16)
C9—C10—H10B 109.8 C20A—C19A—H19A 124.0
H10A—C10—H10B 108.2 C18A—C19A—H19A 124.0
C9A—C10—H10C 108.2 C19A—C20A—S2A 114.2 (15)
N11—C10—H10C 108.2 C19A—C20A—H20A 122.9
C9A—C10—H10D 108.2 S2A—C20A—H20A 122.9
N11—C10—H10D 108.2 N21—C21—C6 177.0 (2)
C2—N1—C1A—N11 172.45 (17) C4—N3—C11—C16 83.5 (6)
C2—N1—C1A—C4A −7.8 (3) C2—N3—C11—C12 73.4 (5)
C1A—N1—C2—N3 −8.3 (3) C4—N3—C11—C12 −101.4 (4)
C1A—N1—C2—S1 172.92 (15) C2—N3—C11—C12A 98.0 (6)
N1—C2—N3—C4 14.5 (3) C4—N3—C11—C12A −76.8 (6)
S1—C2—N3—C4 −166.79 (15) C16A—C11—C12—C13 −14.0 (12)
N1—C2—N3—C11 −159.97 (18) C16—C11—C12—C13 −0.6 (9)
S1—C2—N3—C11 18.8 (3) C12A—C11—C12—C13 101 (2)
C2—N3—C4—O1 177.90 (19) N3—C11—C12—C13 −175.8 (4)
C11—N3—C4—O1 −7.5 (3) C11—C12—C13—C14 −0.9 (10)
C2—N3—C4—C4A −4.2 (3) C12—C13—C14—C15 0.8 (11)
C11—N3—C4—C4A 170.37 (17) C13—C14—C15—C16 0.8 (10)
N1—C1A—C4A—C5 −171.90 (19) C16A—C11—C16—C15 87 (11)
N11—C1A—C4A—C5 7.8 (3) C12—C11—C16—C15 2.3 (10)
N1—C1A—C4A—C4 17.6 (3) C12A—C11—C16—C15 −23.3 (9)
N11—C1A—C4A—C4 −162.66 (17) N3—C11—C16—C15 177.4 (6)
O1—C4—C4A—C5 −3.1 (3) C14—C15—C16—C11 −2.4 (11)
N3—C4—C4A—C5 179.13 (18) C16A—C11—C12A—C13A 6.1 (16)
O1—C4—C4A—C1A 167.1 (2) C16—C11—C12A—C13A 19.7 (10)
N3—C4—C4A—C1A −10.7 (3) C12—C11—C12A—C13A −71.8 (19)
C1A—C4A—C5—C6 −4.3 (3) N3—C11—C12A—C13A −179.9 (6)
C4—C4A—C5—C6 165.48 (18) C11—C12A—C13A—C14A −2.8 (7)
C1A—C4A—C5—C17 174.88 (18) C12A—C13A—C14A—C15A 0.01 (9)
C4—C4A—C5—C17 −15.3 (3) C13A—C14A—C15A—C16A 0.0 (2)
C4A—C5—C6—C6A −2.0 (3) C16—C11—C16A—C15A −83 (11)
C17—C5—C6—C6A 178.80 (18) C12—C11—C16A—C15A 18.6 (12)
C4A—C5—C6—C21 177.59 (19) C12A—C11—C16A—C15A −6.0 (16)
C17—C5—C6—C21 −1.7 (3) N3—C11—C16A—C15A −179.7 (5)
C5—C6—C6A—N7 −177.14 (19) C14A—C15A—C16A—C11 2.9 (8)
C21—C6—C6A—N7 3.3 (3) C4A—C5—C17—C18 115.8 (8)
C5—C6—C6A—N11 4.8 (3) C6—C5—C17—C18 −65.0 (8)
C21—C6—C6A—N11 −174.77 (18) C4A—C5—C17—C18A −78.7 (8)
N11—C6A—N7—C8 −6.0 (3) C6—C5—C17—C18A 100.5 (8)
C6—C6A—N7—C8 175.9 (2) C4A—C5—C17—S2A 117.2 (6)
C6A—N7—C8—C9A 20.3 (11) C6—C5—C17—S2A −63.6 (6)
C6A—N7—C8—C9 −26.7 (3) C4A—C5—C17—S2 −61.0 (3)
N7—C8—C9—C10 56.3 (3) C6—C5—C17—S2 118.17 (19)
C9A—C8—C9—C10 −52.5 (11) C20A—S2A—C17—C18 −10 (7)
N7—C8—C9A—C10 −34 (2) C20A—S2A—C17—C5 177.4 (9)
C9—C8—C9A—C10 55.8 (12) C20A—S2A—C17—C18A 12.5 (13)
C8—C9A—C10—N11 36 (2) C20A—S2A—C17—S2 −4.3 (11)
C8—C9A—C10—C9 −55.6 (12) C20—S2—C17—C18 2.6 (7)
C8—C9—C10—C9A 52.4 (11) C20—S2—C17—C5 180.0 (2)
C8—C9—C10—N11 −55.8 (2) C20—S2—C17—C18A −96 (2)
N7—C6A—N11—C1A −179.30 (19) C20—S2—C17—S2A 1.7 (6)
C6—C6A—N11—C1A −1.2 (3) C5—C17—C18—C19 −179.9 (6)
N7—C6A—N11—C10 7.3 (3) C18A—C17—C18—C19 13.1 (15)
C6—C6A—N11—C10 −174.60 (18) S2A—C17—C18—C19 172 (8)
N1—C1A—N11—C6A 174.77 (18) S2—C17—C18—C19 −2.7 (13)
C4A—C1A—N11—C6A −5.0 (3) C17—C18—C19—C20 1.2 (14)
N1—C1A—N11—C10 −11.7 (3) C18—C19—C20—S2 1.0 (9)
C4A—C1A—N11—C10 168.53 (18) C17—S2—C20—C19 −2.2 (4)
C9A—C10—N11—C6A −23.0 (11) C18—C17—C18A—C19A −17.0 (16)
C9—C10—N11—C6A 23.9 (3) C5—C17—C18A—C19A 174.7 (10)
C9A—C10—N11—C1A 163.4 (11) S2A—C17—C18A—C19A −20.5 (16)
C9—C10—N11—C1A −149.71 (18) S2—C17—C18A—C19A 69 (2)
C2—N3—C11—C16A −87.8 (10) C17—C18A—C19A—C20A 18 (2)
C4—N3—C11—C16A 97.4 (10) C18A—C19A—C20A—S2A −11 (3)
C2—N3—C11—C16 −101.7 (6) C17—S2A—C20A—C19A −1 (2)
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Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
N7—H7···N21i 0.89 (2) 2.14 (2) 2.976 (3) 157 (2)
C9—H9B···O1ii 0.99 2.34 3.197 (3) 144
C16—H16···S2Aiii 0.95 2.73 3.58 (2) 149
C19—H19···S1iv 0.95 2.76 3.652 (5) 156
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Symmetry codes: (i) −x+3, −y+1, −z+2; (ii) −x+3/2, y+1/2, −z+3/2; (iii) x−1, y, z; (iv) −x+3/2, y−1/2, −z+3/2.

Funding Statement

This paper was supported by Baku State University and the RUDN University Strategic Academic Leadership Program.

References

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989024001658/tx2082sup1.cif

e-80-00325-sup1.cif (1.2MB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989024001658/tx2082Isup2.hkl

e-80-00325-Isup2.hkl (314.7KB, hkl)
e-80-00325-Isup3.cml (7.2KB, cml)

Supporting information file. DOI: 10.1107/S2056989024001658/tx2082Isup3.cml

CCDC reference: 2333770

Additional supporting information: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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